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In this paper, a new algorithm, which is the constrained simultaneous iteration reconstruction technique (SIRT), is presented for the inversion of ionospheric electron density. This new algorithm uses the smoothing of neighboring pixels in the same layer to create a reasonable constraint matrix. Thus, it overcomes the limitation of conventional SIRT and improves the accuracy of electron density inversion. The reliability and feasibility of the new algorithm and its superiority to the SIRT are demonstrated by numerical simulation experiment and reconstruction results based on the actual GPS observations.